Slow Spinning Redemption
by Muffy the Dough Slayer
Summary: Sequel to Vindicated. Rated T. MShenko. Saving his clone and offering him a position on the Normandy has certain repercussions. Kaidan's outrage is overshadowed only by Shepard's stubbornness in giving the clone a chance. It's a long road to redemption. The war and Shepard's inability to take care of himself are a full time a job, but one Kaidan's more than willing to accept.
1. Chapter 1

**A/N:** Um... heyyyy guys... so it's been a while since I finished _Vindicated_... months... XD I'm sorry! I had this chapter written for months but lost inspiration, and then I got a new xbox so I lost all my progress on the games. If I want to continue it I'm going to have to play through all 3 of them again which is going to take a while and is very tedious, especially with the first game... even though all I want is like one mission from the 3rd game gahhhh! Achem anywho. So. I have 3 chapters of this story completed, and after that it's going to take a while to update because I have to play through everything again to get the in-game scenes and dialogue right. So... bear with me :)

Note: I'm on AO3 now! I'm "AkuChibi". So... yeah. Some of my original stories plus my ME fanfics are there so far.

Anyway... I don't even know if any of you are still reading this series or not, but here you go ;) The third installment of Medical Red Tape.

Quick recap: My Shepard is default appearance, mostly paragon, Colonist and Sole Survivor background, and is a vanguard.

Main thing to know from the rest of the series if you don't want to read them all (which I recommend...) : Shepard got injured, it was minor but messed with his cybernetics. This eventually led to them having to get shore leave enforced by Hackett. While there they met the clone, Shepard further injured himself with his cybernetics until his system inevitably fried and his heart started giving out on him. He refused to take the clone's heart. Yes the clone is still alive; Brooks is in custody. The clone decided to join them on the Normandy after Shepard had surgery and recovered. Roughly 2 months have passed since the end of _Vindicated._

Chapter length: 3383

Enjoy!

Let us begin!

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><p><strong>Slow Spinning Redemption<strong>

_Sequel to Vindicated - 3rd in Medical Red Tape series_

Written by: Muffy the Dough Slayer

**Warnings:** MShenko slash, rated T for now, canon-typical violence, clones, language, etc. What I usually have, basically. If something new pops up I'll let you know at the beginning of a chapter. Slash, so if that's not your glass of pineapple juice please return to the fridge and try again. Thanks.

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><p>Chapter One<p>

"Commander."

Shepard yawned and rubbed at his eyes from where he sat at his desk, looking over his reports. So far all the numbers were looking good and they were winning the fight in key locations, but he knew the death count was still high and would only continue to rise unless he stopped it. But no pressure or anything, right?

"What, Joker?"

"Your, uh… _twin_ is causing problems in the shuttle bay, sir."

Shepard sighed and pushed to his feet. "Alright. What'd he do _now_?"

He knew letting the clone, _his_ clone, on board wasn't going to be easy but he at least thought he deserved this chance. It had been a week since he'd been allowed on board and already he'd caused at least three fights that Shepard knew about. He didn't think his clone _meant_ to cause such fights but it was hard for the crew to accept him since he'd been trying to kill them not that long ago, trying to take over Shepard's life.

He deserved this chance, though.

"I'm not sure," Joker replied, obvious sigh in his voice. "Should I alert Kaidan?"

Shepard scowled even though he knew his pilot couldn't see him. "No, Joker, I don't think that will be necessary."

Kaidan didn't want the clone on board _at all_. He knew it wouldn't be _easy_ but he hadn't expected Kaidan to react so harshly to the idea of the clone joining them. He'd been under constant surveillance while he was part of the crew, after all, and didn't have free reign over the ship in any way. It was a tentative alliance for the time being. Getting Kaidan to see that, though, proved to be rather difficult.

"Aye, aye, sir," Joker said.

Shepard eased out of his cabin and into the elevator, which he rode down to the shuttle bay. He wasn't entirely sure where Kaidan was but figured he was on deck three, either in med bay or in the mess. He spent a lot of time in both of those places, usually forcing Shepard to go with him.

Ever since that surgery where they infused more cybernetics into his heart, the sentinel made him see Dr. Chakwas every day whether he agreed to go or not. In the end Shepard couldn't deny him anything after all they'd been through and after he'd allowed the clone to come aboard the Normandy, against Kaidan's wishes.

The ride down to shuttle bay was quick enough, and soon he stepped out into violence.

"What's going on?" He didn't quite growl, but he might as well have due to the reaction he got.

His clone, James and Cortez all stopped arguing, James with his fist raised to strike the clone, and turned to look at him. Immediately James dropped his fighting stance and let his arms drop to his sides as he released a heavy sigh while Cortez took a step back, away from the scene.

"Um, well, you see, Loco…"

"He started it," his clone said, tossing the lieutenant a glare.

"I did not! You're the one-"

"Enough!" Shepard snapped, glaring at the two of them while Cortez shuffled off to the side, even though Shepard knew he was far from innocent in all of this. He generally didn't get into fights with his clone but he certainly didn't calm James down, either. "I'm tired of you guys fighting! He's a part of the crew now, Lieutenant, whether you like it or not."

James narrowed his eyes but gave into a slow, stiff nod. He wouldn't outwardly argue with the commander, Shepard knew, but that didn't mean he'd won the battle. Far from it, if the look James tossed toward his look alike was anything to go by, but at least it was stopped for the time being. He'd have to keep a closer eye on his clone, as well as the crew, if he wanted things to go more smoothly.

Shepard looked at his clone. It was still unnerving to stare into a face so similar and yet so _different_, because there was just something about the clone that wasn't the same… something he couldn't entirely place, but it was there all the same, the slight narrowing of the eyes, the darker hue of those blue orbs, so different from when he looked at himself in the mirror. "And _you_! Why do you keep getting into fights? Do you want me to throw you off this ship?"

The clone scowled, Shepard's features shifting darkly. "No."

"Then…?"

"Sorry I'm not _perfect_ like _you_."

Shepard sighed and scrubbed a hand across his face. "You think my life is _perfect_?"

He usually tried not to indulge the clone. But somehow that line got to him. His life was anything but perfect. He _died_ once already, after all. He himself could have easily been a clone as well. He was put in charge of a war when he knew nothing about politics, when he was just one man fighting against many. His life was complicated and difficult and he was _tired_.

No that he expected his clone to understand that, though. Not that he expected _anyone_ to, really. Well… except Kaidan. Kaidan had proven himself rather adept at understanding him, even though Shepard was still a little confused on how and _why_ the man would even _want_ to. That, however, was a topic for another day.

Sighing, he grabbed his clone's arm and hauled him toward the elevator. Thankfully James didn't say anything as they walked away. Once the elevator doors shut, Shepard reached over and pushed a button, causing the elevator to slow to a stop, between floors.

EDI would wonder what was wrong if the elevator stayed like this for very long, but he didn't intend to keep it this way longer than necessary. He just needed a quiet moment to speak with… _himself_, without interruption. Without James sneering in the background; without Kaidan hovering around him.

"How do you like your name?"

He wasn't entirely sure where the question came from, but nevertheless, he went with it and found he did actually want to know the answer.

They couldn't just keep calling him 'clone', after all, so it had been decided that the clone really needed a name, an identity of his own since he'd been denied that before, dubbed a 'clone' right from the start. Shepard in no way agreed with his clone's plans, how he tried to kill him and take over his life, but he could understand it. He knew where he was coming from and with understanding came a certain kind of acceptance.

Blue eyes, identical to his own and yet somehow darker, blinked slowly. "I don't mind it."

Shepard smiled. "I'm glad. Flynn suits you."

In a way, it did. Flynn Shepard. That was the first step in creating his own identity separate from Shepard's. The second was to change his appearance but there was little they could do about that right now unless they dyed his hair or something, but that seemed unnecessary at the moment. Instead they'd given him a different uniform of sorts, more like what they wore on the first Normandy. That was his assigned outfit now and he was only allowed to wear that while Shepard generally wore the new uniforms, or 'casual attire', as Kaidan called the blue jeans and hoodie.

His clone, _Flynn_, smiled somewhat. It was odd to see him smile because he so seldom did it, and when he did, it was only the barest upward twitch of his lips, but it was there all the same. Perhaps only Shepard noticed it and could recognize it for what it was, having grown up with that reflection staring back at him in the mirror.

"Don't worry about the crew," Shepard said. "They'll come around eventually. Not all of them liked me at first, either. It just takes time." He sighed. "In the meantime, _please_ try to keep out of fights."

"And how do you propose I do that?" A delicate brow raised inquisitively.

"Well, for starters, you're gonna be stuck with me for a while," Shepard said, shaking his head. "No one is going to outwardly argue with you and pick a fight if you're with me."

"Your Spectre friend might disagree," Flynn said with this smirk.

"_Kaidan_ isn't someone you need to worry about. Leave him to me."

He pushed the button again and the elevator resumed movement. Best not to tempt EDI, after all. He wasn't exactly watching what floor they were going to, but wasn't entirely surprised when they stopped on deck three instead of deck two and found Kaidan waiting there, arms folded across his chest, foot tapping impatiently as his brown eyes landed on the two of them.

"Hey, Kaidan," Shepard said, smiling at him as he stepped out of the elevator. His clone, Flynn, followed after him even as Kaidan scowled over Shepard's shoulder, watching him. Shepard waved his hand in front of the man, his boyfriend, until those brown eyes shifted toward his face. "Something you need?"

"You're late," the sentinel muttered.

"Late?"

_Didn't know I was on a schedule._

Kaidan's fingers enclosed around his wrist in a light yet firm grip as he turned and led him away from the elevator. "Dr. Chakwas is waiting for you."

Shepard sighed, then, because he hadn't exactly been aware this was a _thing_, now. Was she really going to check him every single day, at nearly the same time? That seemed a little absurd, after all. He was the commander of this ship, leading the war against the Reapers; he didn't have _time_ for this.

He waved Flynn toward the mess while Kaidan drug him through the med bay doors. Dr. Chakwas looked up from her desk as they approached, smiling as she got to her feet. Already her omni-tool blazed orange around her forearm as she lifted her hand, waving it briefly over Shepard's face. Shepard sighed and allowed himself to be scanned, simply thankful it wasn't too invasive this time.

Her tests varied, after all.

Kaidan had yet to release his wrist. Normally Shepard would have said something or lightly pulled away while in the presence of others, but this time he allowed it. She already knew about their relationship anyway, after all. Plus, he didn't really like the thought of continuously hiding it. Thus far they'd told people if they bothered to ask but if they didn't, then they didn't really need to know. It was still technically against the regulations for them to be intimate in any way since Kaidan was his subordinate and he was the commander of this ship, but Shepard didn't care. Regs never bothered him too much before and he wasn't going to let them start now.

Besides, hadn't they all been through enough already? They were in a war, a fight for survival. They could win or lose tomorrow or the next day and he'd rather spend his time not regretting anything than die without allowing himself what he wanted, what everyone wanted. If the Alliance wanted to punish him for it, they could certainly _try_, but he'd been through hell and back for this damn war and he would do what he wanted for the time being.

Dr. Chakwas stepped back, reading the data from her omni-tool. Finally she nodded and looked at him. "Everything seems to be in order," she said.

"See?" Shepard scowled at Kaidan. "You worry too much."

Kaidan rolled his eyes. "It's just a precaution."

Shepard shook his head. "Uh huh. So everything's good, Doc?"

She nodded. "For the time being, yes, but please keep in mind it has only been a little over a week since the operation."

"Trust me, K won't let me forget," Shepard sighed, even as Kaidan's elbow nudged into his ribs, causing him to chuckle as he turned to face the sentinel. "Can we eat now?"

Kaidan sighed. "I guess. I supposed your _clone_ is going to be joining us?"

The distaste twisted the man's face into a scowl, even as Shepard sighed and nodded. "I know you don't like this, but it's the right thing to do."

"I'm not so sure."

"What happened to not doubting me?" Shepard asked, narrowing his eyes. He knew it was a low blow but it instantly had the scowl slipping off Kaidan's face to be replaced with this hesitant expression instead.

"Right," the sentinel sighed, averting his gaze toward the ground. "Sorry."

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><p>Flynn looked up as Shepard and Alenko entered the mess, having left the med bay. Shepard sat across from him at the table while Alenko moved past them, toward the kitchen area. Flynn himself already had a sandwich in his grasp, which he continued to eat despite their presence. A moment later Alenko returned, two sandwiches in hand. He handed one to Shepard and sat next to the man, tossing Flynn a quick glare.<p>

Flynn fought the urge to roll his eyes. Shepard warned him it wouldn't be easy and the crew would probably react negatively to him for a while, but even so, it got a little old, always being treated like the enemy. At one point, yes, he was the enemy. He had his reasons for doing what he did and Shepard claimed to understand them, so why couldn't the rest of the crew? Did the commander not talk to the rest of his crew? Could he not order them to be silent?

What was the point in having that authority if you didn't use the power you got from it?

"Commander."

Flynn didn't flinch when that voice spoke through the comm systems anymore, which was progress. Half the time a part of him still wanted to respond to it, declare that _he _was Commander Shepard, but he managed to shove that part down. He wasn't Commander Ryan Shepard anymore – he was just _Flynn_. It wasn't great, it wasn't horrible, but it was his own, separate identity. Something _Maya_ never gave him.

He didn't like thinking about her, though.

"What is it, Joker?" Shepard sighed, taking a bite out of his sandwich, which was mostly gone by this point.

"Hackett has a job for us, sir."

The commander finished off his sandwich and pushed to his feet with a sigh. "Alright. We're on our way to the war room."

"Aye, aye, sir."

Shepard looked at him, then. "C'mon, you're coming with me."

"What?" Alenko's eyes widened. "Shepard, I don't-"

Shepard managed to silence the man with one quick glare. Flynn got to his feet and followed after the commander as he moved away from the table, toward the elevator. Alenko brought up the rear and Flynn tried to ignore the heat of his gaze forever focused on the back of his head.

They filed into the elevator and rode it up to deck two. Flynn had never been past deck three since he joined Shepard's crew, always forced to stay in the lower areas. He had a bunk in the crew quarters on deck three which was where he slept, but the majority of the rest of his day was either spent in the shuttle bay or in the mess, since it seemed to be where he ran into the least trouble. Trouble still managed to find him, of course, and he'd be lying if he said he didn't enjoy a good fight, but he found he actually wanted to change things. He wanted to simply be a part of a crew, his own individual person instead of Shepard's clone.

That was all anyone saw him as here, though.

For the first time since he joined Shepard, he was led into the war room, Alenko following right behind him. Instead of focusing on the hologram's words – Hackett's words? Was that his name? – he focused on the surrounding crew members. The two tech people working along the outer edge had tense, rigid postures, most likely due to his presence. Alenko, of course, appeared suspicious of his every movement, forever watching him, arms folded across his chest. Shepard, meanwhile, watched Hackett and listened to what was said.

"We'll look into it," Shepard was saying when Flynn tuned back into the conversation. Hackett nodded and the holographic man disappeared.

Shepard turned away from the console, scrubbing a hand across his face.

"Alright," he sighed, "you two suit up. You're coming with me."

"What?" Alenko spluttered, tossing a glance toward Flynn and back. "You can't be serious."

Shepard rolled his eyes. "It'll be fine." His gaze then landed on Flynn. It was still mildly unsettling how similar they looked in every way. "No trouble, right?"

Flynn shrugged. "No promises."

"Shepard-" Alenko said.

Shepard tossed him a quick look. "It'll be fine, Kaidan." He looked back at Flynn. "Kaidan will take you down to the shuttle bay. I expect both of you to be ready in ten minutes. Right, Kaidan?"

Alenko sighed. "Right, Shepard."

A moment later the two walked toward the elevator. Flynn didn't have to be looking back at Alenko to know his every move was being watched. The man's eyes might as well have been little suns burning holes in the back of his head.

He was surprised Shepard was allowing him to go on this mission, since everyone here was so uneasy around him. It was unsettling for himself as well, because everyone here thought he was going to betray them in some way. He'd be lying if he said it hadn't crossed his mind, but it was either this or jail. He never actually thought Shepard would take him on missions, though. At least not this soon.

He knew he'd be under constant surveillance, but he couldn't help but think of ways to escape the scrutiny and leave this group, this ship. As much he didn't like the thought of jail and whatnot, he didn't particularly like it here, either. Perhaps he could leave and start his own life somewhere…

Except, he had no idea how to go about doing that. In his short life, all he knew was hunting down Shepard and stealing his life. It was all Maya would allow him to think about, and his whole life thus far revolved around that. This gave him a new identity, sure, but no one could see past his resemblance to Shepard, and what he did in the past.

"No trouble," Alenko said once they stepped out of the elevator, now in the shuttle bay.

Flynn fought the urge to roll his eyes. "Yeah, sure, whatever."

No trouble? No promises. After all, every little thing he did was considered as _trouble_, right?

_Still a prisoner either way._

Better than a jail cell? Sure.

But it was a prison all the same.

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><p>Kaidan couldn't foresee any of this going well. The clone couldn't be trusted, especially not this early. Convincing Shepard of this was more complicated than one would think.<p>

The clone, Flynn, steered cleared of most of the crew but still wound up in a lot of fights, verbal or otherwise. Thus far he'd been nothing but trouble. He'd tried to tell Shepard this wasn't a good idea, but the man could be very stubborn.

Hopefully things would turn out okay. According to Hackett this was a simple mission, but they'd been told that before. Their intel was less than great. Surely there were other crews who could do these little missions, right?

He couldn't fight it, though. At least this way they were doing something instead of waiting around, but sometimes Kaidan wondered if they were really being productive. Then again, they were helping people who would otherwise most likely be ignored. So it couldn't be all bad, right?

He looked over as the elevator door opened to reveal Shepard walking toward them. He was already dressed in his N7 armor and Cortez was already in the shuttle, waiting for them to board. Shepard nodded at them and they all climbed into the shuttle.

Kaidan wondered if they got this mission because they were so close to the target location. It only took ten minutes, after all.

As the shuttle took off, though, he couldn't help but wonder if Shepard was mistaken this time… if it was really smart to trust the clone…

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><p><strong>AN:** And there's that chapter. Like I said, it was written months ago. Hope it still sounds okay! I was worried about it which is why I never posted it... but oh well. Thanks for reading and as always, PLEASE REVIEW :D

~Muffy the Dough Slayer~


	2. Chapter 2

**A/N:** Hey, guys. I'm debating about uploading the next chapter yet seeing as how it's all that's written so far. I can't write more of this story, after chapter 3, until I play through the games again and that's going to take a while since I don't have as much free time as I used to. So, we'll see how that goes. So If this story goes quiet for a while, don't be surprised. Also, I wanted to add in-game dialogue and scenes in here like in the previous stories, but I would have had to play through the games again to get this mission and everything, so instead I just took what I remembered from the mission. So I know it's not perfect. And it's mostly description since I don't know any in-game dialogue off the top of my head. Anyway, hope it still sounds okay.

Chapter length: 3599

Onward!

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><p>Chapter Two<p>

The mission was simple. Or, at least, it was supposed to be. Things rarely went their way, though, so Kaidan wasn't optimistic, especially with the clone coming with them. He couldn't believe Shepard was allowing this. He still hated that the clone was even aboard the Normandy, but there was little he could do about it. It was Shepard's decision and try as he might to convince him to put the clone back in jail, his efforts never worked. Once Shepard's mind was set on something, that was it.

He kept an eye on the clone, walking between him and Shepard with the commander leading the way and Kaidan bringing up the rear. He was ready to leap into action at any moment should the clone try something.

Everything was going smoothly for the time being. Eden Prime wasn't exactly his favorite place in the world due to the circumstances surrounding the last time they visited, with the Prothean beacon and Sovereign, along with Saren. Everything went to hell after that, so yeah, this wasn't one of his favorite locations.

Shepard's clone didn't act like he knew this place. He didn't have Shepard's memories, though. At least that much was certain. Or, if he even had the slightest inkling of his memories, of this place, his face gave nothing away. But Kaidan was leaning toward the former.

It was quiet for a while. They weren't sure what they were looking for, except some Prothean artifact. Liara wanted to come, of course, since her life was dedicated to discovering more about the Protheans, which had put her on their radar in the first place. It was also the initial reason for her attraction to Shepard – because he'd been 'touched' by the beacon. Memories of that were very clear in his mind despite the fact it happened years ago. He'd been pushed out of the way, after all. It should have been him the beacon hit, not Shepard. But, as Shepard was want to do, he threw himself in the way and the explosion from the beacon that followed still echoed through Kaidan's mind.

At first he'd thought Shepard dead and wasn't sure how to feel about it. They weren't friends, but they weren't enemies, either. Shepard saving him like that was a step along the road to friendship.

But back on track, shrugging the thoughts away, Liara wanted to come. Shepard left her behind for her safety; even though she was a natural biotic, she wasn't very adept at fighting. If forced into the situation, she could hold her own for a little while, but she had little training in that area. It made sense to leave her behind.

What _didn't_ make sense was Shepard bringing the clone with them.

For a while they walked in silence.

The silence was broken only when shots were fired. The next instant, the three of them were behind cover, near a few upscale homes that were small but cozy. He looked around the room only after the gunfire receded momentarily as Shepard and clone returned fire. Bodies remained inside, slaughtered. He looked around, swallowing thickly as he took notice of the mug on the coffee table, the plates and papers on the table in the small kitchen, and people strewn around the couch in front of a screen.

_These people were just sitting down… minding their business… They weren't soldiers._

He wasn't aware a growl escaped him until Shepard tossed him a quick glance.

Cerberus went too far this time. Too _far_.

Attacking people involved with the military, that wasn't okay but it wasn't totally uncalled for, either. Attack random civilians… slaughtering them in their homes… without warning…

_Not okay._

That wasn't okay in the slightest.

A voice crackled over the comm in his ear. It was so sudden he stiffened, unaware the gunfire had stopped until then. Quickly he looked around but Shepard was okay, standing in front of him, looking down at him expectantly. Just behind him stood the clone, scowling down at him.

Two very different expression from very similar faces. It was more than a little unnerving.

He barely heard what was said through the earpiece, so outraged at the fact these poor people were murdered like this. There was no reason to do something like this, and Cerberus went too far. Way too far. This was… This was unfathomable. Unforgiveable. Just terrible all around. Anger burned through him, a hot ember he couldn't cool, but he tried to do so as Shepard left the small house in which they'd taken cover. He swallowed and followed after him and the clone as they walked away, toward an outward cliff-edge. There was something sitting on top of it though he couldn't make it out from here.

As they got closer it looked to be some kind of old yet advanced pod. Confusion knocked against his mind, cooling some of the anger. There was writing along the side he couldn't read but recognized almost instantly. A chill inched up his spine as Shepard stepped toward it curiously.

LIara's voice echoed through his head via the comm. "It's not a Prothean device," she said, voice in awe much as it had been when she first met Shepard after his run in with the Prothean beacon. "It's a living Prothean!"

Kaidan froze, then, staring at the pod.

_It couldn't be…_

Right? That wasn't possible. Even if it _was_ a Prothean, it wouldn't be alive. 50,000 years had passed since their time! Not even a species as advanced as the Protheans could live that long.

She told them not to attempt to break it open as it would kill the Prothean inside. Just as he was trying to wrap his mind around the fact she thought this Prothean was still _alive_, Shepard walked away from the pod, his clone trailing after him with that perpetual scowl on his face. Kaidan followed after glancing again at the pod.

They hadn't made it very far when a bullet whizzed past his face and he spun into cover, just as Shepard and his clone did the same. More gunfire ensued but slowly they managed to make some ground, entering yet another home, searching for something but he'd spaced out at the part, still in shock over the Prothean.

_Something new every day._

Except this was pretty crazy, even by their standards.

"Shepard?"

He wasn't aware he was alone until then. Shepard's clone poked his head out of a side room, scowling at him. Kaidan followed him back into the room and found Shepard standing in front of a large screen. Nothing but vague images and symbols flashed across it and he sighed, certain this was broken and they'd have to find another one if they wanted to open the pod. He reached out to grab Shepard's shoulder when the commander stiffened as though sensing his touch.

Shepard usually never stiffened at his touch. Come to think of it, he wasn't really moving, or blinking. Kaidan's mind flashed back to the geth consensus with Legion, Shepard entering the virtual reality.

"Shepard?" he asked, but his voice wasn't very loud. He took in a breath and tried again, his hand landing on Shepard's shoulder. "Commander?"

"He can't hear you," the clone said.

Kaidan's gaze snapped toward him briefly. Irritation sparked through him like it always did when he saw the clone. "How do you know?" he snapped. "What'd you do?"

Surely this clone had done something to him. Shepard had been fine before Kaidan lost track of him. Guilt gnawed at him for being so distracted, but this place had that effect on him. He vowed to do better, but first he needed to see what was wrong with Shepard.

From a physical standpoint he didn't appear to be in pain. He just had this vague, detached expression on his face, the faintest of frowns tugging his lips downward. Kaidan walked around until he stood in front of him, watching him. He was breathing fine, but his body was rigid and unmoving, as were his eyes.

"What'd you do?" he spat at the clone, shooting a glare toward him.

"Nothing," the clone spat back. "He just went stiff when the thing started playing. You know more about this than I do."

Kaidan swallowed because technically that was true. Kaidan had been around Shepard longer, been a part of the crew longer, been fighting the Reapers longer… If anyone knew what happening here, it would be Kaidan, and yet he had absolutely no idea.

He felt lost, but he was finding that was a common feeling when dealing with Shepard. The man panicked him just as often as he comforted him. It was a ping-pong match of give and take that always left his lungs unable to expand enough for him to catch his breath, his mind racing with anticipation.

Almost as though a switch had been flipped, Shepard's body relaxed and he blinked at Kaidan, who stood directly in front of him with a hand still resting firmly on his shoulder.

"Hey," Shepard said. "Did you see that?"

"See what?" Kaidan asked, frowning. "Are you okay?"

"I'm fine," Shepard said. "Why?"

"You were a statue for a minute," the clone sighed. "Alenko overreacted. Are we done here?"

If looks could kill the clone would have been six feet under, but as it was Kaidan shifted his gaze back toward the Shepard he cared about. "What'd you see?" he asked quietly as his eyes did a mental assessment of Shepard's well-being.

Physically he seemed fine. Breaths weren't harsh or shaky, pupil's weren't dilated, he wasn't favoring one side or grimacing in pain…

_So what's wrong with him? What happened?_

Two questions he wanted answered, but it would have to wait as _more_ gunfire cut off their conversation. A second later the clone was flying out of the room with this _laugh_ as he shot back at the Cerberus troops. The sound left a chill slithering around Kaidan's spine, slowly spindling up it as he looked back at Shepard. Shepard lifted his forgotten rifle and moved toward the doorway. A bullet whizzed by his right ear and slammed into the wall behind him.

Kaidan swallowed and followed him as he vaulted out of the room, over a kitchen table and landed near a window, ducking beneath it for cover.

"How many of these guys are there?" he wondered aloud, unaware he'd spoken the words until he got a response.

"Doesn't matter," the clone said, shooting over his own cover.

The words didn't register as much as that grin on his face did. He was actually _enjoying_ this. Enjoying the fight.

Shepard was at home on the battle field. This both terrified and relieved Kaidan for various reasons. That didn't mean, however, that he enjoyed fighting. His clone, on the other hand, was another matter entirely.

Strange how two people could be so alike and yet so _different_.

_How did I ever think he was the real Shepard…_

In hindsight he should have known better. This clone may have looked like Shepard in a lot of ways, but not in the ways that mattered. Not in the eyes or the smile or any of his movements. Not in the way he talked or went about a situation. This just further proved he should have _known_. He could have saved both him and Shepard a lot of pain had he realized it sooner; maybe Shepard wouldn't have even needed that surgery to keep him _alive_.

_Nothing you can do about it now._

He took a breath and continued firing.

* * *

><p>Flynn honestly couldn't care less about what was happening or the <em>why<em> of the fighting. Fighting was in his blood – either naturally or unnaturally. If it was natural, Shepard was very good at hiding it. The thrill of the fight was intoxicating and let him forget about the fact he was a _clone_ and didn't _belong_ and shouldn't _exist_. It was hard to forget those thoughts because everyone aboard the Normandy, apart from Shepard and Chakwas, kept reminding him.

Shepard didn't remind him because for some reason, he gave him this opportunity. Chakwas didn't remind him because she was a doctor and was forced to detach herself from the patient and situation to treat people without judgment.

So, yes, fighting was good. It helped better than any medicine could.

It almost let him forget the fact Alenko kept glaring holes in the back of his head. Why that still bothered him, in the heat of battle, he'd never know. Not that it mattered.

"Okay, _okay_," Alenko growled, "you can stop shooting now."

Flynn blinked, unaware the enemy was gone. The troops were dead along the ground. The thrill of the fight ebbed away and he automatically followed the first person to walk past him, which was Shepard. Of course it was. Alenko never led the way and Flynn had no idea where he was going.

They searched through a few more of those houses. The bodies strewn along the ground were easy to step over.

They eventually found another hidden room and entered it without a problem. No more troops came along. The screen blinked to life with those odd symbols again, and once again Shepard stared at it and went stiff. At least this time Alenko didn't immediately turn to him and blame him. That was getting old.

Eventually Shepard snapped out of whatever trance he was in, once again asked if they could see it to which they replied no, and they left the room as though nothing happened. Alenko and Shepard whispered to each other, probably about what just happened. He followed after them with a sigh, keeping a good distance between them.

As they tried to exit the house, more gunfire echoed through the air and he was once again lost in the frenzy of the fight. Slowly they moved forward, making ground through the enemies. He lost track of how many he killed, but the number didn't matter.

The fight ended too soon for his liking and they returned to the pod. There was something interesting about the pod, or at least there was supposed to be but he had no idea what it was. Not that it mattered.

He didn't have an earpiece, after all. Because he technically wasn't part of the _crew_.

_Second chance my ass. _

Apparently what Shepard learned – or saw – from those screens was a code to open the pod. Why, then, could he not see it too? They were essentially the same person. Except, he didn't really have Shepard's memories. Perhaps that was why he was the reject, the back-up for when _perfect_ Shepard needed something.

Bitterness was bad coffee in his mouth but that was okay. He was used to that by now, the taste knocking against his teeth, swirling around his tongue and burning down his throat.

Eventually, after some more gunfire and several more dead troops (seriously, what the hell? Did Cerberus breed them like rabbits?) the pod finally hissed and opened. Shepard stood over it as he was want to do. Alenko approached his side while Flynn stayed back. Being forced onto the sidelines was certainly not what he'd been expecting this mission. Perhaps more of a hostile approach since this was his first mission with the crew, especially with how much Alenko disliked him. There were very few sharp comments, though, and apart from the occasional angry looks the major shot him, it was like he wasn't even there. In all honesty, he wasn't sure what to think about that.

At least being glared and growled at was at least _acknowledgement_ of his existence; this was like he was nothing. A ghost among shadows, an echo of a life that never was but could have been.

He swallowed down the bad coffee and watched as steam rose from the pod. Not steam, he realized, but frozen air but too warm to be solid. Several minutes ticked by as nothing happened. He sighed, certain this was a bust. They should return to the Normandy. He could leave without them, but then he'd be stranded here. The pilot, dubbed Joker though he wasn't sure why, wouldn't double back for him or let him aboard without Shepard and Alenko. If he left he'd be stranded with nowhere to go, no one to miss him or acknowledge him or-

A green creature with a big head crawled out of the pod, staggering. A wave of _something_ slammed into Alenko and Shepard, knocking them backward toward Flynn. Sensing a fight, Flynn stepped forward, biotics itching to attack. He wasn't sure why Shepard's hand on his arm stopped him, but it did and he stopped moving forward. For now. Shepard stepped toward the creature instead. Flynn assumed it to be a Prothean since that was why they were after, but he had no working knowledge on the subject. All those thoughts belonged to Shepard.

Shepard's hand landed on the creature's shoulder. Flynn recognized it as a comforting, placating gesture, used to ease a situation. He had seen the movement used numerous times since his arrival, usually with Alenko. The reaction with Alenko was smooth and calming; his shoulders drooped, his eyes softened in that way they never did for Flynn (only harsh glares for him, expression stony). The reaction with this creature was sudden.

Both Shepard and the creature stiffened in unison. A spark of _something_ flashed between them. For a moment it was like being back in those rooms, staring blankly at a screen etched with strange symbols. Alenko stepped forward and the moment broke, silence snapping apart as though it were a physical sound.

Shepard's eyes were somewhat wild. Flynn was used to seeing those eyes (his own and yet not his own) aloft with various attempts at humor, guarded when approaching him about his fights, and even those exhausted droops of his eyelids when he refused to accept Flynn's heart to save himself. Perhaps that was why this expression got to him – it was one he had not seen. If he himself ever wore it, he did not know, and _Maya_ never told him anything.

Thinking about her was wrong and he quickly brushed those thoughts away, along with the burst of bad coffee pressing against his tongue.

"What was that?" Alenko asked.

There was a lilt to his voice Flynn recognized. Never used for him, but it conveyed worry and regret and a multitude of other emotions he didn't recognize. Reserved for Commander Shepard, and not Clone Shepard.

Not that he cared. It would just be nice if someone looked at him like that, sometimes. Instead of like he was a prisoner, free to move but shut down in spirit. He wasn't sure which was worse.

"Did you see that?" Shepard asked again.

_Obviously not,_ Flynn wanted to say. _We haven't yet._

But he bit his tongue and said nothing. Shepard was the only one who gave him a chance; the only one even remotely on his side. Arguing with him certainly wouldn't help matters and might only make things worse. He couldn't stand it, he was sure, if _everyone_ on the ship looked at him with anger and hate and that swirling mess of conflicted emotions he didn't recognize because he never saw.

_Maya's_ looks were swift and fleeing, a sly grin here, a smirk there, but always her gaze strayed away from him. If she met his eyes it wasn't for long. She often spoke of Shepard – _Commander_ Shepard, whom she wanted him to destroy and take over his life. He never questioned her motives; why would he? He himself had reasons for attempting to overthrow Shepard and steal his life. A stolen life was better than no life at all.

He took a breath and released it slowly. Thoughts of that time in his short life were better left in the dark, with the bad coffee.

Shepard was talking but he wasn't really listening. Something about a pick-up. A moment later the Kodiak shuttle appeared. Flynn moved toward it automatically. If he didn't get on at the same time as Alenko and Shepard, he was certain he would be left behind. The pilot of the shuttle, Cortez, might say it was an accident; he thought everyone was on board because he wasn't used to seeing two Shepards. Once upon a time he might have believed that, but not after the looks. The anger. The fights. The way Cortez always took Vega's side of their arguments when _Vega_ was the one to start them, not him. The way the man stood silent in the background, not outwardly expressing his disapproval but doing little to stop the upcoming fight, either.

He wasn't aware he'd climbed aboard the shuttle until he sat on the bench in the back, squished between Shepard and the cool wall, Alenko on Shepard's other side. Their new guest (if one could call it that) sat on the other, smaller bench behind the pilot's chair, which could, in theory, only seat one. It wasn't even technically a seat.

The ride back to the Normandy was spent in silence. Flynn was used to silence by now, of course, but this silence wasn't thick and heavy, coated in tension and anger burning just beneath. No, this silent was quiet and pensive, used for thinking instead of stewing.

He relaxed marginally against the cool surface, certain no fights would be coming along this ride, verbal or otherwise. When they got back to the Normandy was another matter entirely.


	3. Chapter 3

**A/N:** Sorry for the delay, guys. I've had this chapter done for a while but didn't want to post it until I was going to start writing this story again. I just finished playing the second game, so I will be starting on the 3rd again soon, which means this story can finally be updated :) Just have to get to that part of the game, sigh. Anyway, I have a lot of plans for other Mass Effect stories, some of them AU and some of them canon, as well as plans for a way to end this series, maybe xD We will see, though. Right now I'm just trying to play through them again. But be on the look-out for a story with Shepard as an engineer.

Also ~ for the next story I might write, with that engineer I mentioned, I am debating about who love interest could be. Should it be A) Kaidan; B) Joker; or C) original character I've been toying with that might be fun... Please let me know, yes? This engineer character story would start with ME1 and go through AU-ish events of ME2, ultimately ending in ME3 with a twist. Soooo yeah. Let me know, please!

Anyway this is getting long...

Chapter length: 2553

Onward!

* * *

><p>Chapter Three<p>

_Javik. A living Prothean._

To be honest, Shepard wasn't all that shocked. After all, he met his clone on the Citadel; nothing really surprised him anymore after that. This, though. This came close. He'd gone down to Eden Prime expecting to find an artifact; they did that a lot, searching for old ruins and artifacts to potentially help them in building the Crucible, which, last he'd heard, was still missing a key component. While it wasn't outwardly stated that he needed to find said component, it was generally assumed.

_Of course._

Exhaustion was a familiar feeling; an old friend wrapping him in a thick, uneasy hug. He wanted to give into it as much as he wanted to fight it.

He managed to stay awake and alert long enough to speak with the Prothean, Javik. He was nothing like Shepard expected. From Liara's tales, the Protheans were larger than life, highly advanced and peaceful. Javik contradicted everything she said. If anything he was probably a jerk; at least now, but according to him, it was how they all acted back then. Shepard could understand it; Javik said he was born into the war with the Reapers, after all. For a century their war lasted. Their war was just beginning.

So, being a little rude and lacking a little tact wasn't all that surprising. His knowledge about the room's previous occupant, however, was.

He knew Grunt was there without anyone telling him. It almost made Shepard smile, how he summed up Grunt's emotions in the room. At the time, with Grunt, it hadn't been funny; the krogan had been a little out of control, attempting to kill Shepard while simultaneously attempting to explain himself. He'd never been born; he didn't know what to expect. Puberty was raw and new and everything every guy, no matter the species, feared.

A complete and utter lack of control. Conflicting emotions, too rapid to decipher. Physical changes. Combine it all and anyone could act like a krogan.

Listening to Javik talk was as interesting as it was… he didn't want to say _boring_ because it was something that might help them and it was interesting, but it did manage to lull him into an almost-slumber, in which he still walked and talked but his mind had all but shut down. His movements, his words, were on autopilot.

He was as grateful as he was startled when warm, familiar hands clutched his shoulders, turning him in the direction of the elevator. He walked into it automatically, the heat of that warm body pressing against his back. One hand left his shoulder, leaving him shivering with the loss of such warmth, before it returned and the elevator began moving.

"No offense," Kaidan said easily, his voice soothing in a way no meds or pillows could offer, "but you kind of look like hell."

"I do not," Shepard said with a scowl, his automatic response because he was _fine_. Absolutely, completely _fine_. It'd be great if people would stop worrying about his health. He was better now that he'd had that surgery; it was much easier to breathe, easier than it'd been _before_ shore leave on the Citadel. He was fine.

"Uh huh."

Shepard sighed as the doors opened. He stepped out, followed by Kaidan who had yet to release him, and pushed open the door to the captain's cabin. _His_ cabin, though he was no captain. Every time he entered he couldn't help but wonder why it wasn't _Anderson's_ cabin, why the man stayed on Earth. He understood the need to fight on Earth; of course he did. He'd wanted to stay too. But he was no good at politics; it would have made much more sense if he stayed on Earth and Anderson took charge of the Normandy.

Of course, he realized as Kaidan guided him toward the bed, had he stayed on Earth, nothing would have been fixed and improved with Kaidan. And perhaps that was worth it; worth his lack of tact and political prowess.

He wasn't lying when he said he wasn't sure what he'd do without Kaidan.

"_You'll never find out,"_ was Kaidan's response.

He hoped so.

"Hey."

He blinked, unaware he'd been so trapped in his thoughts. He hadn't been aware of hands winding down his sides, careful extracting him from his uniform. The shirt was first to go, which was halfway off before he cleared his thoughts enough to realize what was happening. Kaidan's fingers were swift and efficient, movements treading along a familiar road.

"Where'd you go?"

Shepard almost chuckled, remembering him saying the same thing back at the apartment, before everything exploded into chaos. That last day of peace before the clone knocked Kaidan out and attempted to kill him.

"Nowhere," Shepard breathed, but it was a little hard to talk with Kaidan's lips peppering his neck with quick, tiny kisses, barely there before they moved onto the next spot. He reached out, tangling a hand in the soft black hair which was somewhat spiky at the top – he really needed to ask him about that – and used what leverage that gave him to lightly pull the sentinel more toward him.

Kaidan's reply was a breathy laugh as he all but tripped into Shepard's lap. Shepard wasn't complaining, though. With his other hand he wrapped his arm around Kaidan, lightly lifting the edge of his shirt. A question and an invitation.

Kaidan's smile left him grinning. It always did, somehow.

The hand on his chest, lightly pushing him down, left him breathless and irritated because he knew that movement. Knew it wasn't for more intimate proceedings but rather things which irritated him because he was _fine_.

"Sleep," Kaidan said quietly.

"You're the one who decided to undress me."

Amber brown eyes rolled, glistening in the light, the water reflected from the small ripples in the fish tank which took up one entire wall despite the fact there were no fish in it. "I was trying to make you more _comfortable_," he said almost petulantly, like Shepard was a kid who simply couldn't understand.

Shepard rolled his eyes in much the same way as Kaidan as the sentinel easily rolled off and away from him. The warmth dissipated as their contact was severed and he sighed, scrubbing a hand across his face.

"Besides," Kaidan replied with an easy grin which left Shepard quirking a brow, "you're tired for any fun anyway."

"You saying I'm not fun, Major?"

"Never said that, Commander," Kaidan said.

"So I'm fun?" he asked, sitting up.

Kaidan chuckled. "Never kiss and tell."

"But we didn't kiss," Shepard said, "so there's nothing to tell."

Kaidan's response was to lower his head enough to reach Shepard's – Shepard was only half sitting up, palms stretched off to his sides to leverage him up enough – and their lips met in this gentle yet meaningful touch. It was light and soft and important all in one, something he'd grown to expect from Kaidan.

That didn't stop him from dragging the sentinel down onto him again.

Kaidan's attempts to argue were quickly silenced by a tongue flicking against his lips.

* * *

><p>Javik was… irritating, if Flynn had to choose a word to describe him. He steered clear of the Prothean when possible, but inevitably their paths crossed. He was on clean-up duty with Vega and they were to check all of the rooms, including Javik's.<p>

Cleaning wasn't fun; neither was being partnered with Vega.

To be fair, everything was going okay for the time being. Vega gave him the usual quick glares whenever they saw each other. He returned them with a quick, dead stare of his own, and they went about business as usual. Vega was put on clean-up duty for picking a fight with him again; Flynn was stuck with him for pretty much the same reason. He couldn't see this ending well.

_It's okay. If he tries anything, it'll be the last thing he does._

There would be no one around to intervene should things get out of hand. He'd had enough of Vega's callous words, biting remarks and even those agile fists slamming into him. He could easily overtake the man; he was a biotic, after all. Vega was strong, but he was biotic strong.

Attempting to attack Vega in such a way would be met with quick reproach and disgust. He'd seen enough of that already, so he decided to play nice for the time being. Unless Vega started something; then all bets were off.

Originally he had no plans and no desire to see the Prothean. Even Alenko found him a little _off_, according to what he'd overheard earlier in the mess before he and Shepard shuffled away and toward the elevator.

So he had no idea what to expect.

"Another primitive," Javik sighed upon their arrival. He didn't bid them goodbye, a quick dismissal, but nor did he invite them in.

They lingered in the doorway for a moment before Flynn sighed and stepped through the entryway. Vega followed after him, mop in hand. Flynn himself hauled the large bucket, which slopped water over the sides with each large, irritated step. Javik's eyes stared at him in this disapproving way, but that was okay. He was used to it by now so he just ignored him and put the bucket down in the center of the room. If that was right next to where Javik decided to sit and meditate – or whatever it was he was doing – that wasn't his problem.

"Sorry for the interruption," Vega said. "Loco – I mean, Commander Shepard – wanted us to clean up a little."

"He assumes me to be messy."

It was said as a shocked statement and not a question, so he didn't bother replying. Instead he gestured for Vega to dip the mop into the bucket. Vegan tossed him a quick glare and all but threw the mop at him. He caught it with ease and sighed; he knew it would be this way, working with the man. At least it was something to do, though, so he got to work on mopping.

"He's just thorough," Vega was saying. "No disrespect, I'm sure."

He did sound certain. How he could have such faith was beyond Flynn. After all, no one ever said that about _him_, and he was the same as Shepard. Well… No. Not really. They only looked the same. What was it Shepard said, sitting alone with him in C-Sec?

"_You can't clone everything."_

Right. That.

Yet another thing he didn't share.

He'd never shared anything before, except the looks, voice and name of a man he never knew until very recently. He'd only been awake six months before he'd decided to take back a life that was, in theory, his and yet not his at the same time.

Waking was a shock; learning he was a clone was worse. Maya attempted to help him, though now, looking back, he wondered if it was just a façade, an attempt to lure him to her side for her own, unknown motives.

_Always ulterior motives._

He took a breath and continued mopping while Vega and Javik talked in the background. He tuned them out easily enough, focusing instead at the task at hand. It was so much easier than thinking about anything else.

_Keep occupied and don't get into trouble._

That was his easiest way off this ship and away from C-Sec. Do his 'time', be good, and get 'released' and do whatever the hell he wanted with a life he technically didn't deserve to have.

Getting away from here, away from everything, was what he ultimately wanted. Right? Away from the lies and betrayal, the fact he was a clone, away from _Shepard_ and everything he wasn't but could have been in another life…

He wasn't aware his hands were trembling, however slightly, until Vega tossed him a quick, uneasy glance. It wasn't harsh this time, or angry, just curious and slightly disturbed. He found he liked that even less.

He tightened his grip on the mop and continued working.

* * *

><p>"Hey."<p>

Kaidan looked up from his reports and smiled as Shepard approached him, plate in hand. They were currently in the mess. It technically wasn't the _best_ place to do his reports, but he liked the people and movement more than the emptiness of his old room, the Observation Room. Normally he wouldn't mind it; now he did. He blamed Shepard.

"Hey," he said in return as Shepard sat across from him, "how'd it go?"

Shepard scowled, stabbing a fork into the meat on his plate. Kaidan wasn't sure what today's special was, but it didn't look like human food. It didn't smell bad, though. "Hackett was _fascinated_ by Javik," he said with a heavy sigh which meant the talk had been tiring, but not that it hadn't gone well. "Liara looks like he kicked her puppy." He held a hand up. "No, I don't want to hear it. I know she would say 'that metaphor doesn't apply here' and blah, blah, blah, I don't care."

Kaidan smirked. "That bad, huh?"

The look Shepard gave him left him almost laughing. Almost. He swallowed it down before it could escape.

"I don't know what's worse," Shepard said, "Javik or Hackett… or Liara and her constant questions."

Kaidan shrugged. "It's her life's work, and he just turned it all upside down and told her she was wrong," he said quietly. "I'd be upset too."

Shepard sighed and shook his head, pushing his food around his plate. "How are the reports going?"

"Fine," Kaidan said. "Almost done."

Blue eyes lifted to meet his. "I don't suppose a sanity check would be appropriate after today, would it?"

He chuckled. "It just might."

He should argue, deny it; there wasn't time for this and Shepard might regret it later if something went wrong aboard the ship or with their next mission. Distraction's weren't good in the middle of a war. He hoped he was a good distraction, though, and not the bad kind.

He should say no. Argue. Last night he tried to put up a fight but got lost somewhere along the way. His 'no, Shepard' turned into 'yes' and '_Ryan_' very fast and there was little he could do once he was lost in it.

So he should say no; Shepard was tired. Despite what he said, he was still healing.

He was exhausted; anyone would be in his position. Finding a member of a species previously thought completely wiped out would make anyone a little tired.

But he couldn't say no – never could.

Shepard abandoned his plate when he was halfway done. Kaidan wanted to tell him to keep eating because somewhere along the way, he lost track of how much the commander was actually eating and consuming. The two didn't share meals all the time anymore, Shepard busy in the war room or keeping his clone in line, and Kaidan doing his reports and tracking down his old students and attempting to help wherever he could. This had them on different schedules sometimes, so the time they did spend together, they didn't really spend _eating_.

He vowed to check over how much he was eating right after Shepard stopped nibbling on his ear.

Because, yeah, that was pretty distracting.

* * *

><p><strong>AN:** And there's that. Please let me know about what I asked! Thanks for reading and please review :3

~Muffy the Dough Slayer~


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